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8d4d

gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes

Method: ELECTRON MICROSCOPY Dmax: 219.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADP-ribosylation factor 1

Homo sapiens

UniProt P84077

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain C； UniProt 2–181 Chain D； UniProt 2–181 Chain F； UniProt 2–181 Chain H； UniProt 2–181 Not recorded Protein Nef × 4 （Q90VU7） HLA class I histocompatibility antigen, A alpha chain × 2 （P04439） AP-1 complex subunit beta-1 × 2 （Q10567） AP-1 complex subunit gamma-1 × 2 （P22892） AP-1 complex subunit mu-1 × 2 （P35585） AP-1 complex subunit sigma-3 × 2 （Q96PC3） GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments. cryo-EM vitrification conditions：Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted. Resolution 9.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8D4D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HUR HUMAN ADP-RIBOSYLATION FACTOR 1 COMPLEXED WITH GDP, FULL LENGTH NON-MYRISTOYLATED Deposited 1995-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–180（180 aa）
Chain B 1–180（180 aa）
Not recorded MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.309
1U81 Delta-17 Human ADP Ribosylation Factor 1 Complexed with GDP Deposited 2004-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 17–180（164 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SOLUTION NMR
NMR measurement conditions pH 7；305 K；Ionic strength (raw mmCIF value) 50mM salt；Pressure ambient
NMR measurement conditions pH 7；301 K；Ionic strength (raw mmCIF value) 50mM salt；Pressure ambient
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50mM salt；Pressure ambient
NMR sample composition 10mM KPO4, 50mM NaCl, 1mM MgCl2, 5mM NaN3, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 7.5% (w/v) etherbicelle in 10mM KPO4, 50mM NaCl, 1mM MgCl2, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 4% pentaethylene glycol octylether in 10mM KPO4, 50mM NaCl, 1mM MgCl2, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
3O47 Crystal structure of ARFGAP1-ARF1 fusion protein Deposited 2010-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 11–181（171 aa） Fragment：ARF1GAP, UNP residues 1-140, ARF1, UNP residues 11-181
Not recorded ZN ZINC ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；20% PEG-3350, 0.2M trilithium sulfate, pH not applicable, vapor diffusion, temperature 291K
Resolution 2.80 Å R-free 0.243
3O47 Crystal structure of ARFGAP1-ARF1 fusion protein Deposited 2010-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 11–181（171 aa） Fragment：ARF1GAP, UNP residues 1-140, ARF1, UNP residues 11-181
Not recorded ZN ZINC ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；20% PEG-3350, 0.2M trilithium sulfate, pH not applicable, vapor diffusion, temperature 291K
Resolution 2.80 Å R-free 0.243
4HMY Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1 Deposited 2012-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 17–181（165 aa） Fragment：UNP residues 17-181
Mutation：Q71L GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；288 K；0.2M lithium sulfate, 0.1M Tris pH 8.5, 0.2M lithium nitrate, 0.7M ammonium sulphate, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 7.00 Å R-free 0.250
6CM9 Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit Deposited 2018-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 17–181（165 aa） Fragment：UNP residues 17-181
Chain H 17–181（165 aa） Fragment：UNP residues 17-181
Mutation：Q71L Mutation：Q71L GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
6CRI Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer Deposited 2018-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 24 PDB declaration: 24-meric
Chain C 17–181（165 aa）
Chain H 17–181（165 aa）
Chain K 17–181（165 aa）
Chain L 17–181（165 aa）
Chain U 17–181（165 aa）
Chain V 17–181（165 aa）
Mutation：Q71L Mutation：Q71L Mutation：Q71L Mutation：Q71L Mutation：Q71L Mutation：Q71L GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6D83 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer monomeric subunit Deposited 2018-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain C 17–181（165 aa）
Chain H 17–181（165 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
6D84 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer Deposited 2018-04-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain C 17–181（165 aa）
Chain H 17–181（165 aa）
Chain I 17–181（165 aa）
Chain N 17–181（165 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
6DFF Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer Deposited 2018-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain C 17–181（165 aa）
Chain H 17–181（165 aa）
Mutation：Q71L Mutation：Q71L GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6FAE The Sec7 domain of IQSEC2 (Brag1) in complex with the small GTPase Arf1 Deposited 2017-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 18–181（164 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M tris 16% PEG 8K 0.1M Potassium chloride
Resolution 2.35 Å R-free 0.285
7DN8 Crystal structure of Salmonella effector SopF in complex with ARF1 Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 17–181（165 aa）
Mutation：Q71L MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10.5% PEG 3350, 120mM alpha-ketoglutarate, 100mM Tris-HCl pH 8.0
Resolution 2.61 Å R-free 0.240
7DN8 Crystal structure of Salmonella effector SopF in complex with ARF1 Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 17–181（165 aa）
Mutation：Q71L MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10.5% PEG 3350, 120mM alpha-ketoglutarate, 100mM Tris-HCl pH 8.0
Resolution 2.61 Å R-free 0.240
7DN8 Crystal structure of Salmonella effector SopF in complex with ARF1 Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 17–181（165 aa）
Mutation：Q71L MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10.5% PEG 3350, 120mM alpha-ketoglutarate, 100mM Tris-HCl pH 8.0
Resolution 2.61 Å R-free 0.240
7DN8 Crystal structure of Salmonella effector SopF in complex with ARF1 Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 17–181（165 aa）
Mutation：Q71L MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10.5% PEG 3350, 120mM alpha-ketoglutarate, 100mM Tris-HCl pH 8.0
Resolution 2.61 Å R-free 0.240
7DN9 Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1 Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 17–181（165 aa）
Mutation：Q71L NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；13% PEG 3350, 300mM sodium citrate, 100mM Bis-Tris pH 6.5
Resolution 3.29 Å R-free 0.277
7DN9 Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1 Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 17–181（165 aa）
Mutation：Q71L NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；13% PEG 3350, 300mM sodium citrate, 100mM Bis-Tris pH 6.5
Resolution 3.29 Å R-free 0.277
7DN9 Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1 Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 17–181（165 aa）
Mutation：Q71L NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；13% PEG 3350, 300mM sodium citrate, 100mM Bis-Tris pH 6.5
Resolution 3.29 Å R-free 0.277
7DN9 Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1 Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 17–181（165 aa）
Mutation：Q71L NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；13% PEG 3350, 300mM sodium citrate, 100mM Bis-Tris pH 6.5
Resolution 3.29 Å R-free 0.277
7MGE Structure of C9orf72:SMCR8:WDR41 in complex with ARF1 Deposited 2021-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 17–180（164 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.94 Å
7R4H phospho-STING binding to adaptor protein complex-1 Deposited 2022-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 17–181（165 aa）
Chain H 17–181（165 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UX3 Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 2–181（180 aa）
Chain H 2–181（180 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.60 Å
8D4C beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-06-01 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain C 2–181（180 aa）
Chain D 2–181（180 aa）
Chain F 2–181（180 aa）
Chain H 2–181（180 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.30 Å
8D4E Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 2–181（180 aa）
Chain H 2–181（180 aa）
Chain Z 2–181（180 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.20 Å
8D4F beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain C 2–181（180 aa）
Chain D 2–181（180 aa）
Chain F 2–181（180 aa）
Chain H 2–181（180 aa）
Chain Q 2–181（180 aa）
Chain Z 2–181（180 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.80 Å
8D4G gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain C 1–181（181 aa）
Chain D 1–181（181 aa）
Chain F 1–181（181 aa）
Chain H 1–181（181 aa）
Chain Q 1–181（181 aa）
Chain Z 1–181（181 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 11.60 Å
8D9R AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain 3 2–181（180 aa）
Chain 4 2–181（180 aa）
Chain 5 2–181（180 aa）
Chain 6 2–181（180 aa）
Chain 7 2–181（180 aa）
Chain C 2–181（180 aa）
Chain H 2–181（180 aa）
Chain J 2–181（180 aa）
Chain K 2–181（180 aa）
Chain O 2–181（180 aa）
Chain P 2–181（180 aa）
Chain Q 2–181（180 aa）
Chain X 2–181（180 aa）
Chain Z 2–181（180 aa）
Chain a 2–181（180 aa）
Chain b 2–181（180 aa）
Chain c 2–181（180 aa）
Chain d 2–181（180 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
8D9U AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain C 2–181（180 aa）
Chain H 2–181（180 aa）
Chain J 2–181（180 aa）
Chain K 2–181（180 aa）
Chain O 2–181（180 aa）
Chain P 2–181（180 aa）
Chain Q 2–181（180 aa）
Chain X 2–181（180 aa）
Chain Z 2–181（180 aa）
Chain a 2–181（180 aa）
Chain b 2–181（180 aa）
Chain c 2–181（180 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9W beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain F 2–181（180 aa）
Chain I 2–181（180 aa）
Not recorded MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.30 Å
8RSQ Crystal structure of marine actinobacteria clade rhodopsin (MAR) - human GTPase Arf1 (L8K,Q71L) chimera; Ground state Deposited 2024-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–181（180 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 LFA EICOSANE × 8 RET RETINAL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；2.0 M Ammonium Phosphate buffer
Resolution 2.30 Å R-free 0.263
8RSR Crystal structure of marine actinobacteria clade rhodopsin (MAR) - human GTPase Arf1 (L8K,Q71L) chimera; N state Deposited 2024-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–181（180 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 LFA EICOSANE × 1 OLA OLEIC ACID × 1 RET RETINAL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；2.0 M Ammonium Phosphate
Resolution 2.30 Å R-free 0.282
8SDW Crystal structure of the non-myristoylated mutant [L8K]Arf1 in complex with a GDP analogue Deposited 2023-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–181（181 aa）
Mutation：L8K G3D GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277.15 K；0.2 M Sodium nitrate, 20% w/v Polyethylene glycol 3,350, pH 6.8
Resolution 1.75 Å R-free 0.210
9C58 AP-3 bound to myristoylated Arf1 (Q71L) Deposited 2024-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 2–181（180 aa）
Mutation：Q71L MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；1x PBS (pH 7.4), 300mM NaCl, 1mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Commercialized version - Chameleon
Resolution 4.70 Å
9C59 Human AP-3 dimer bound to myristoylated Arf1 (Q71L) and LAMP1 cargo on a lipid nanodisc Deposited 2024-06-06 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 2–181（180 aa）
Chain C 2–181（180 aa）
Chain a 2–181（180 aa）
Chain c 2–181（180 aa）
Mutation：Q71L Mutation：Q71L Mutation：Q71L Mutation：Q71L MG MAGNESIUM ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；1x PBS (pH 7.4), 300 mM NaCl, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Commercialized version - Chameleon
Resolution 4.30 Å
9C5A AP-3 Arf1 dimeric interface, focused refinement Deposited 2024-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 2–181（180 aa）
Chain c 2–181（180 aa）
Mutation：Q71L Mutation：Q71L MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；1x PBS (pH 7.4), 150mM NaCl, 1mM TCEP, 2mM GTP, 5mM EDTA, 10mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Commercial form of the chameleon (SPT Labtech)
Resolution 4.20 Å
9C5B AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map Deposited 2024-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 2–181（180 aa）
Chain C 2–181（180 aa）
Mutation：Q71L Mutation：Q71L MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；1x PBS (pH 7.4), 300mM NaCl, 1mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Commercialized version - chameleon
Resolution 4.50 Å
9QLO NMT1-NAC bound human RNC with full length ARF1 - State 1 Deposited 2025-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain CZ 2–181（180 aa）
Not recorded MG MAGNESIUM ION × 191 G3D GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
9QLP NMT1-NAC bound human RNC with full length ARF1 - State 2 Deposited 2025-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain CZ 2–181（180 aa）
Not recorded MG MAGNESIUM ION × 191 G3D GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
9QLQ NMT1-NAC bound human RNC with full length ARF1 - alternative State Deposited 2025-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain CZ 2–181（180 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
9QPQ The structure of the COPI leaf bound to GOLPH3 Deposited 2025-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain R 1–181（181 aa）
Chain S 1–181（181 aa）
Chain T 1–181（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.50 Å
9RTW Mammalian AP3 complex on tubular membranes (AP3 centered) Deposited 2025-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 15–181（167 aa）
Chain F 15–181（167 aa）
Chain G 15–181（167 aa）
Chain H 15–181（167 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.40 Å
9RTX Mammalian AP3 complex on tubular membranes (ARF1 centered Beta3-ARF1 dimer-Beta3 interface) Deposited 2025-07-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain E 1–181（181 aa）
Chain F 1–181（181 aa）
Chain G 1–181（181 aa）
Chain H 1–181（181 aa）
Chain I 1–181（181 aa）
Chain J 1–181（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.50 Å
9RTY Mammalian AP3 complex on tubular membranes (ARF1 centered Beta3-ARF1 dimer-Delta interface) Deposited 2025-07-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain E 1–181（181 aa）
Chain F 1–181（181 aa）
Chain G 1–181（181 aa）
Chain H 1–181（181 aa）
Chain I 1–181（181 aa）
Chain J 1–181（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.90 Å
9RTZ Mammalian AP3 complex on tubular membranes (ARF1 centered Delta-ARF1 dimer-Delta3 interface) Deposited 2025-07-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain E 1–181（181 aa）
Chain F 1–181（181 aa）
Chain G 1–181（181 aa）
Chain H 1–181（181 aa）
Chain I 1–181（181 aa）
Chain J 1–181（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 13.00 Å
9U9R ARF1(Q71L) bound M4-CTD-undocked AP-4 core Deposited 2025-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 18–181（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 6.60 Å
9U9S ARF1(Q71L) bound M4-CTD-docked AP-4 core Deposited 2025-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 18–181（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 6.80 Å

39 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 1–180； UniProt 2–181 Author chain D； PDBConstruct 1–180； UniProt 2–181 Author chain F； PDBConstruct 1–180； UniProt 2–181 Author chain H； PDBConstruct 1–180； UniProt 2–181

Protein Nef

Human immunodeficiency virus 1

UniProt Q90VU7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain I； UniProt 2–206 Chain K； UniProt 2–206 Chain L； UniProt 2–206 Chain N； UniProt 2–206 Not recorded ADP-ribosylation factor 1 × 4 （P84077） HLA class I histocompatibility antigen, A alpha chain × 2 （P04439） AP-1 complex subunit beta-1 × 2 （Q10567） AP-1 complex subunit gamma-1 × 2 （P22892） AP-1 complex subunit mu-1 × 2 （P35585） AP-1 complex subunit sigma-3 × 2 （Q96PC3） GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments. cryo-EM vitrification conditions：Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted. Resolution 9.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8D4D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4EMZ HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain) Deposited 2012-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–206（206 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Microbatch underoil；pH 6.5；298 K；0.1M HEPES, 3% PEG8000, pH 6.5, Microbatch underoil, temperature 298K
Resolution 2.90 Å R-free 0.278
4EMZ HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain) Deposited 2012-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–206（206 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Microbatch underoil；pH 6.5；298 K；0.1M HEPES, 3% PEG8000, pH 6.5, Microbatch underoil, temperature 298K
Resolution 2.90 Å R-free 0.278
4EN2 HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain) Deposited 2012-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–206（206 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch underoil；pH 6.5；298 K；0.1M HEPES, 3% PEG8000, pH 6.5, microbatch underoil, temperature 298K
Resolution 2.58 Å R-free 0.258
4EN2 HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain) Deposited 2012-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–206（206 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch underoil；pH 6.5；298 K；0.1M HEPES, 3% PEG8000, pH 6.5, microbatch underoil, temperature 298K
Resolution 2.58 Å R-free 0.258
4NEE crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef Deposited 2013-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 63–203（141 aa） Fragment：HIV-1 Nef, residues 54-203
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；288 K；70mM CHES pH 9.5, 140mM NaCl, 7% PEG8000, 21% glycerol, 0.2mM inositol hexakisphosphate (IP6), VAPOR DIFFUSION, SITTING DROP, temperature 288K
Resolution 2.88 Å R-free 0.267
4NEE crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef Deposited 2013-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 63–203（141 aa） Fragment：HIV-1 Nef, residues 54-203
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；288 K；70mM CHES pH 9.5, 140mM NaCl, 7% PEG8000, 21% glycerol, 0.2mM inositol hexakisphosphate (IP6), VAPOR DIFFUSION, SITTING DROP, temperature 288K
Resolution 2.88 Å R-free 0.267
4NEE crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef Deposited 2013-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 63–203（141 aa） Fragment：HIV-1 Nef, residues 54-203
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；288 K；70mM CHES pH 9.5, 140mM NaCl, 7% PEG8000, 21% glycerol, 0.2mM inositol hexakisphosphate (IP6), VAPOR DIFFUSION, SITTING DROP, temperature 288K
Resolution 2.88 Å R-free 0.267
4NEE crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef Deposited 2013-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 63–203（141 aa） Fragment：HIV-1 Nef, residues 54-203
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；288 K；70mM CHES pH 9.5, 140mM NaCl, 7% PEG8000, 21% glycerol, 0.2mM inositol hexakisphosphate (IP6), VAPOR DIFFUSION, SITTING DROP, temperature 288K
Resolution 2.88 Å R-free 0.267
6CM9 Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit Deposited 2018-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain L 1–206（206 aa） Fragment：Tetherin UNP residues 2-21, Nef UNP residues 1-206
Chain N 1–206（206 aa） Fragment：Tetherin UNP residues 2-21, Nef UNP residues 1-206
Chain T 1–206（206 aa） Fragment：Tetherin UNP residues 2-21, Nef UNP residues 1-206
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
6CRI Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer Deposited 2018-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 24 PDB declaration: 24-meric
Chain N 1–206（206 aa） Fragment：Tetherin UNP residues 2-26, Nef UNP residues 1-206
Chain T 1–206（206 aa） Fragment：Tetherin UNP residues 2-26, Nef UNP residues 1-206
Chain Y 1–206（206 aa） Fragment：Tetherin UNP residues 2-26, Nef UNP residues 1-206
Chain Z 1–206（206 aa） Fragment：Tetherin UNP residues 2-26, Nef UNP residues 1-206
Chain c 1–206（206 aa） Fragment：Tetherin UNP residues 2-26, Nef UNP residues 1-206
Chain d 1–206（206 aa） Fragment：Tetherin UNP residues 2-26, Nef UNP residues 1-206
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6D83 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer monomeric subunit Deposited 2018-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain L 1–206（206 aa） Fragment：Tetherin UNP residues 2-21, Nef UNP residues 1-206
Chain T 1–206（206 aa） Fragment：Tetherin UNP residues 2-21, Nef UNP residues 1-206
Mutation：L164A, L165A Mutation：L164A, L165A GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
6D84 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer Deposited 2018-04-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain L 1–206（206 aa） Fragment：Tetherin UNP residues 2-21, Nef UNP residues 1-206
Chain O 1–206（206 aa） Fragment：Tetherin UNP residues 2-21, Nef UNP residues 1-206
Chain R 1–206（206 aa） Fragment：Tetherin UNP residues 2-21, Nef UNP residues 1-206
Chain T 1–206（206 aa） Fragment：Tetherin UNP residues 2-21, Nef UNP residues 1-206
Mutation：L164A, L165A Mutation：L164A, L165A Mutation：L164A, L165A Mutation：L164A, L165A GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
6DFF Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer Deposited 2018-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain L 1–206（206 aa）
Chain T 1–206（206 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6URI HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex Deposited 2019-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain N 26–206（181 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 6.9；298 K；15% Peg 4000, 0.2M potassium chloride, ~10% 1,6-hexanediol, 0.1M HEPES
Resolution 3.00 Å R-free 0.277
7UX3 Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain L 2–206（205 aa）
Chain N 2–206（205 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.60 Å
8D4C beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-06-01 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain I 2–206（205 aa）
Chain K 2–206（205 aa）
Chain L 2–206（205 aa）
Chain N 2–206（205 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.30 Å
8D4E Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain L 2–206（205 aa）
Chain N 2–206（205 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.20 Å
8D4F beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain I 1–206（206 aa）
Chain K 1–206（206 aa）
Chain L 1–206（206 aa）
Chain N 1–206（206 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.80 Å
8D4G gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain I 1–206（206 aa）
Chain K 1–206（206 aa）
Chain L 1–206（206 aa）
Chain N 1–206（206 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 11.60 Å
8D9R AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain L 2–206（205 aa）
Chain N 2–206（205 aa）
Chain e 2–206（205 aa）
Chain f 2–206（205 aa）
Chain g 2–206（205 aa）
Chain h 2–206（205 aa）
Chain i 2–206（205 aa）
Chain o 2–206（205 aa）
Chain p 2–206（205 aa）
Chain q 2–206（205 aa）
Chain r 2–206（205 aa）
Chain s 2–206（205 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
8D9S AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain L 2–206（205 aa）
Chain N 2–206（205 aa）
Chain e 2–206（205 aa）
Chain f 2–206（205 aa）
Chain g 2–206（205 aa）
Chain h 2–206（205 aa）
Chain i 2–206（205 aa）
Chain o 2–206（205 aa）
Chain p 2–206（205 aa）
Chain q 2–206（205 aa）
Chain r 2–206（205 aa）
Chain s 2–206（205 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9T AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain L 2–206（205 aa）
Chain N 2–206（205 aa）
Chain d 2–206（205 aa）
Chain e 2–206（205 aa）
Chain f 2–206（205 aa）
Chain g 2–206（205 aa）
Chain h 2–206（205 aa）
Chain n 2–206（205 aa）
Chain o 2–206（205 aa）
Chain p 2–206（205 aa）
Chain q 2–206（205 aa）
Chain r 2–206（205 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9U AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain L 2–206（205 aa）
Chain N 2–206（205 aa）
Chain d 2–206（205 aa）
Chain e 2–206（205 aa）
Chain f 2–206（205 aa）
Chain g 2–206（205 aa）
Chain h 2–206（205 aa）
Chain n 2–206（205 aa）
Chain o 2–206（205 aa）
Chain p 2–206（205 aa）
Chain q 2–206（205 aa）
Chain r 2–206（205 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9V gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes Deposited 2022-06-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain I 1–206（206 aa）
Chain K 1–206（206 aa）
Chain L 1–206（206 aa）
Chain N 1–206（206 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.40 Å
8D9W beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes Deposited 2022-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain N 1–206（206 aa）
Chain U 1–206（206 aa）
Chain V 1–206（206 aa）
Chain d 1–206（206 aa）
Not recorded MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.30 Å

20 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q90VU7_9HIV1
Isoform —
PDB entities 2
Chains and sequence ranges Author chain I； PDBConstruct 1–205； UniProt 2–206 Author chain K； PDBConstruct 1–205； UniProt 2–206 Author chain L； PDBConstruct 1–205； UniProt 2–206 Author chain N； PDBConstruct 1–205； UniProt 2–206

HLA class I histocompatibility antigen, A alpha chain

Homo sapiens

UniProt P04439

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain P； UniProt 334–365 Chain Y； UniProt 334–365 Mutation：T345S, S349G, G355S, C363A ADP-ribosylation factor 1 × 4 （P84077） Protein Nef × 4 （Q90VU7） AP-1 complex subunit beta-1 × 2 （Q10567） AP-1 complex subunit gamma-1 × 2 （P22892） AP-1 complex subunit mu-1 × 2 （P35585） AP-1 complex subunit sigma-3 × 2 （Q96PC3） GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments. cryo-EM vitrification conditions：Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted. Resolution 9.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8D4D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2XPG Crystal structure of a MHC class I-peptide complex Deposited 2010-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa） Fragment：HEAVY CHAIN, RESIDUES 25-298
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.1 M BIS-TRIS-PROPANE, PH 8.0, 0.2 M NA/K PHOSPHATE, 20% (V/V) PEG3350
Resolution 2.60 Å R-free 0.247
3RL1 HIV RT derived peptide complexed to HLA-A*0301 Deposited 2011-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa） Fragment：residues in UNP 25-298
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.00 Å R-free 0.222
3RL2 HIV Nef derived peptide Nef73 complexed to HLA-A*0301 Deposited 2011-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa） Fragment：residues in UNP 25-298
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2M calcium acetate hydrate, 0.1M Sodium cacodylate trihydrate, 18%(w/v) Polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.39 Å R-free 0.265
6ENY Structure of the human PLC editing module Deposited 2017-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 25–365（341 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.80 Å
6O9B Crystal structure of HLA-A3*01 in complex with a wild-type beta-catenin peptide Deposited 2019-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–304（280 aa） Fragment：UNP residues 25-304
Not recorded PG4 TETRAETHYLENE GLYCOL × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 IMD IMIDAZOLE × 2 PEG DI(HYDROXYETHYL)ETHER × 4 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1 M MES/imidazole, pH 6.5, 0.03 M diethylene glycol, 0.03 M triethylene glycol, 0.03 M tetraethylene glycol, 0.03 M pentaethylene glycol, 20% PEG500 MME, 10% PEG20000
Resolution 2.20 Å R-free 0.227
6O9C Crystal structure of HLA-A3*01 in complex with a mutant beta-catenin peptide Deposited 2019-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–304（280 aa） Fragment：UNP residues 25-304
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 SO4 SULFATE ION × 10 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1 M MES, pH 6.5, 0.2 M ammonium sulfate, 30% PEG5000 MME
Resolution 2.45 Å R-free 0.259
7L1B Crystal structure of HLA-A*03:01 in complex with a wild-type PIK3CA peptide Deposited 2020-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；10.00 % w/v Polyethylene glycol 8,000, 200 mM Calcium acetate, 100 mM HEPES; pH 7.5
Resolution 2.04 Å R-free 0.221
7L1C Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide Deposited 2020-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa）
Not recorded GOL GLYCEROL × 5 FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；277.15 K；20% w/v Polyethylene glycol 3,350, 200 mM Ammonium formate, pH 6.6
Resolution 1.96 Å R-free 0.205
7L1D Crystal structure of human 21LT2-2 TCR bound to HLA-A*03:01 in complex with a mutant PIK3CA peptide Deposited 2020-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–298（274 aa）
Not recorded ACT ACETATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；10% w/v Polyethylene glycol 8,000, 200mM Magnesium acetate
Resolution 3.11 Å R-free 0.250
7MLE Crystal Structure of HLA-A*03:01 in complex with VVRPSVASK, an 9-mer epitope from Influenza B virus Deposited 2021-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–301（277 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；1M trisodium citrate, 0.1M sodium cacodylate pH 6.5
Resolution 2.20 Å R-free 0.264
7PHR Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I Deposited 2021-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: undecameric
Chain H 25–304（280 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
7QPD Structure of the human MHC I peptide-loading complex editing module Deposited 2022-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain M 25–365（341 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
7RK7 The complex between TIL 1383i TCR and human Class I MHC HLA-A2 with the bound Tyrosinase(369-377)(N371D) nonameric peptide Deposited 2021-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–299（275 aa） Fragment：UNP residues 25-299
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；16% PEG 3350, 2% tacsimate, 100mM Tris (pH 8.5)
Resolution 2.54 Å R-free 0.255
7RM4 Neoantigen p53R175H-specific TCR 6-11 binds to p53R175H-HLA-A2 Deposited 2021-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–299（275 aa） Fragment：UNP residues 25-299
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris propane (pH 8.5), and 0.2 M Potassium thiocyanate
Resolution 3.33 Å R-free 0.295
7RM4 Neoantigen p53R175H-specific TCR 6-11 binds to p53R175H-HLA-A2 Deposited 2021-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 25–299（275 aa） Fragment：UNP residues 25-299
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris propane (pH 8.5), and 0.2 M Potassium thiocyanate
Resolution 3.33 Å R-free 0.295
7RM4 Neoantigen p53R175H-specific TCR 6-11 binds to p53R175H-HLA-A2 Deposited 2021-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain K 25–299（275 aa） Fragment：UNP residues 25-299
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris propane (pH 8.5), and 0.2 M Potassium thiocyanate
Resolution 3.33 Å R-free 0.295
7RM4 Neoantigen p53R175H-specific TCR 6-11 binds to p53R175H-HLA-A2 Deposited 2021-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 25–299（275 aa） Fragment：UNP residues 25-299
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris propane (pH 8.5), and 0.2 M Potassium thiocyanate
Resolution 3.33 Å R-free 0.295
7RRG Crystal structure of human 0606T1-2 TCR bound to HLA-A*03:01 in complex with a mutant PIK3CA peptide Deposited 2021-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–298（274 aa）
Not recorded GOL GLYCEROL × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；12% w/v Polyethylene glycol 3,350, 100 mM Succinic acid
Resolution 2.12 Å R-free 0.221
7STF Structure of KRAS G12V/HLA-A*03:01 in complex with antibody fragment V2 Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–304（280 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
7UC5 Crystal Structure of HLA A*0301 in complex with ILRGSVAHK, a 9-mer epitope from Influenza A Deposited 2022-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–301（277 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.2 Ammonium Sulfate, 0.1 Bis-Tris propane pH 6.5, 22% PEG 3350
Resolution 1.95 Å R-free 0.229
7UC5 Crystal Structure of HLA A*0301 in complex with ILRGSVAHK, a 9-mer epitope from Influenza A Deposited 2022-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 25–301（277 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.2 Ammonium Sulfate, 0.1 Bis-Tris propane pH 6.5, 22% PEG 3350
Resolution 1.95 Å R-free 0.229
7UX3 Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain Y 334–365（32 aa）
Mutation：T345S, S349G, G355S, C363A GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.60 Å
8D4C beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-06-01 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain P 334–365（32 aa）
Chain Y 334–365（32 aa）
Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.30 Å
8D4E Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain Y 334–365（32 aa）
Mutation：T345S, S349G, G355S, C363A GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.20 Å
8D4F beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain P 334–365（32 aa）
Chain Y 334–365（32 aa）
Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.80 Å
8D4G gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain P 334–365（32 aa）
Chain Y 334–365（32 aa）
Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 11.60 Å
8D9R AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain 0 334–365（32 aa） Fragment：MHC-I cytosolic tail (HLA-A/B)
Chain 1 334–365（32 aa） Fragment：MHC-I cytosolic tail (HLA-A/B)
Chain 2 334–365（32 aa） Fragment：MHC-I cytosolic tail (HLA-A/B)
Chain Y 334–365（32 aa） Fragment：MHC-I cytosolic tail (HLA-A/B)
Chain y 334–365（32 aa） Fragment：MHC-I cytosolic tail (HLA-A/B)
Chain z 334–365（32 aa） Fragment：MHC-I cytosolic tail (HLA-A/B)
Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
8D9S AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain 0 334–365（32 aa）
Chain 1 334–365（32 aa）
Chain 2 334–365（32 aa）
Chain Y 334–365（32 aa）
Chain y 334–365（32 aa）
Chain z 334–365（32 aa）
Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9T AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain 0 334–365（32 aa）
Chain 1 334–365（32 aa）
Chain Y 334–365（32 aa）
Chain x 334–365（32 aa）
Chain y 334–365（32 aa）
Chain z 334–365（32 aa）
Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9U AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain 0 334–365（32 aa）
Chain 1 334–365（32 aa）
Chain Y 334–365（32 aa）
Chain x 334–365（32 aa）
Chain y 334–365（32 aa）
Chain z 334–365（32 aa）
Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9V gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes Deposited 2022-06-11 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain P 334–365（32 aa） Fragment：MHC-I cytosolic tail (HLA-A/B)
Chain Y 334–365（32 aa） Fragment：MHC-I cytosolic tail (HLA-A/B)
Mutation：T345S, S349G, G355S, C363S Mutation：T345S, S349G, G355S, C363S GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.40 Å
8D9W beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes Deposited 2022-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain Y 334–365（32 aa）
Chain j 334–365（32 aa）
Mutation：T345S, S349G, G355S, C363A Mutation：T345S, S349G, G355S, C363A MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.30 Å
8DVG Structure of KRAS WT(7-16)-HLA-A*03:01 Deposited 2022-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–304（280 aa） Fragment：UNP residues 25-304
Not recorded SO4 SULFATE ION × 13 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M ammonium sulfate 0.1M sodium cacodylate pH 6.5 30 % w/v PEG 8,000
Resolution 2.59 Å R-free 0.228
8K4T Crystal structure of HLA-A*11:01 in complex with KRAS G12C peptide (VVVGACGVGK) Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Ammonium sulfate,Sodium cacodylate pH 6.0, PEG 4000
Resolution 2.30 Å R-free 0.316
8K4T Crystal structure of HLA-A*11:01 in complex with KRAS G12C peptide (VVVGACGVGK) Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Ammonium sulfate,Sodium cacodylate pH 6.0, PEG 4000
Resolution 2.30 Å R-free 0.316
8K4V Crystal structure of HLA-A*11:01 in complex with KRAS G12R peptide (VVVGARGVGK) Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Ammonium sulfate, Sodium cacodylate, PEG 4000
Resolution 3.10 Å R-free 0.347
8K4V Crystal structure of HLA-A*11:01 in complex with KRAS G12R peptide (VVVGARGVGK) Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Ammonium sulfate, Sodium cacodylate, PEG 4000
Resolution 3.10 Å R-free 0.347
8K4V Crystal structure of HLA-A*11:01 in complex with KRAS G12R peptide (VVVGARGVGK) Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Ammonium sulfate, Sodium cacodylate, PEG 4000
Resolution 3.10 Å R-free 0.347
8K4V Crystal structure of HLA-A*11:01 in complex with KRAS G12R peptide (VVVGARGVGK) Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Ammonium sulfate, Sodium cacodylate, PEG 4000
Resolution 3.10 Å R-free 0.347
8K50 Crystal structure of HLA-A*11:01 in complex with KRAS G12V peptide (VVVGARGVGK) Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Ammonium sulfate, Sodium cacodylate, PEG 4000
Resolution 2.80 Å R-free 0.281
8K50 Crystal structure of HLA-A*11:01 in complex with KRAS G12V peptide (VVVGARGVGK) Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Ammonium sulfate, Sodium cacodylate, PEG 4000
Resolution 2.80 Å R-free 0.281
8K50 Crystal structure of HLA-A*11:01 in complex with KRAS G12V peptide (VVVGARGVGK) Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Ammonium sulfate, Sodium cacodylate, PEG 4000
Resolution 2.80 Å R-free 0.281
8K50 Crystal structure of HLA-A*11:01 in complex with KRAS G12V peptide (VVVGARGVGK) Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Ammonium sulfate, Sodium cacodylate, PEG 4000
Resolution 2.80 Å R-free 0.281
8RNI HLA-A*03:01 with KRAS-G12V-10mer Deposited 2024-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–301（277 aa）
Not recorded GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1M ammonium citrate tribasic pH7, 12% PEG 3350
Resolution 2.49 Å R-free 0.276
8RRO G12V-TCR complex with HLA-A3 Deposited 2024-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 25–302（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.1M Bis-Tris Propane (pH 6.5), 0.2M Na2SO4, 14-20% PEG 3350
Resolution 3.50 Å R-free 0.286
8RRO G12V-TCR complex with HLA-A3 Deposited 2024-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 25–302（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.1M Bis-Tris Propane (pH 6.5), 0.2M Na2SO4, 14-20% PEG 3350
Resolution 3.50 Å R-free 0.286
8RRO G12V-TCR complex with HLA-A3 Deposited 2024-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain M 25–302（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.1M Bis-Tris Propane (pH 6.5), 0.2M Na2SO4, 14-20% PEG 3350
Resolution 3.50 Å R-free 0.286
8RRO G12V-TCR complex with HLA-A3 Deposited 2024-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 25–302（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.1M Bis-Tris Propane (pH 6.5), 0.2M Na2SO4, 14-20% PEG 3350
Resolution 3.50 Å R-free 0.286
8RRO G12V-TCR complex with HLA-A3 Deposited 2024-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain W 25–302（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.1M Bis-Tris Propane (pH 6.5), 0.2M Na2SO4, 14-20% PEG 3350
Resolution 3.50 Å R-free 0.286
8RRO G12V-TCR complex with HLA-A3 Deposited 2024-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain b 25–302（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.1M Bis-Tris Propane (pH 6.5), 0.2M Na2SO4, 14-20% PEG 3350
Resolution 3.50 Å R-free 0.286
8RRO G12V-TCR complex with HLA-A3 Deposited 2024-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain g 25–302（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.1M Bis-Tris Propane (pH 6.5), 0.2M Na2SO4, 14-20% PEG 3350
Resolution 3.50 Å R-free 0.286
8RRO G12V-TCR complex with HLA-A3 Deposited 2024-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain l 25–302（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.1M Bis-Tris Propane (pH 6.5), 0.2M Na2SO4, 14-20% PEG 3350
Resolution 3.50 Å R-free 0.286
8RYM Structure of S2 TCR in complex with HLA-A*03:01 bound to ELFSYLIEK peptide Deposited 2024-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；50 mM HEPES pH 7.0, 13 % w/v PEG 8000
Resolution 2.34 Å R-free 0.272
8RYO Structure of S2-198 TCR in complex with HLA-A*03:01 bound to ELFSYLIEK peptide Deposited 2024-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–299（275 aa）
Not recorded TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL × 1 EDO 1,2-ETHANEDIOL × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；50 mM MOPS pH 6.7, 14 % w/v PEG 8000
Resolution 2.05 Å R-free 0.244
8RYP Structure of S8 TCR in complex with HLA-A*03:01 bound to ELFSYLIEK peptide Deposited 2024-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–299（275 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；50 mM Magnesium acetate, 20 mM MOPS pH 7.2, 50 mM Sodium chloride, 12 % w/v PEG 8000
Resolution 1.81 Å R-free 0.241
8UDR Structure of the P1B7 antibody bound to the Sotorasib-modified KRas G12C peptide presented by the A*03:01 MHC I complex Deposited 2023-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–299（275 aa）
Not recorded MOV AMG 510 (bound form) × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM HEPES ph 7.5, 100 mM KCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VCL Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide Deposited 2023-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa）
Not recorded FMT FORMIC ACID × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277.15 K；12% w/v Polyethylene glycol 3,350, 4% v/v TacsimateTM, pH 6.0
Resolution 2.40 Å R-free 0.230
8VJZ HLA-A*03:01 with WT KRAS-10mer Deposited 2024-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–301（277 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1M ammonium citrate tribasic pH7, 12% PEG 3350
Resolution 1.90 Å R-free 0.214
8VR9 Structure of a synthetic antibody in complex with a class I MHC presenting a hapten-peptide conjugate Deposited 2024-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–299（275 aa） Fragment：extracellular domain
Not recorded MOV AMG 510 (bound form) × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
8VRA Structure of a synthetic antibody in complex with a class I MHC presenting a hapten-peptide conjugate Deposited 2024-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–299（275 aa）
Not recorded MOV AMG 510 (bound form) × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9ASF Crystal structure of HLA-A*03:01 in complex with a wild-type PIK3CA peptide analogue (Trp-6 Bta) Deposited 2024-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa） Fragment：extracellular domain
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；15% w/v Polyethylene glycol 6,000, 50 mM Potassium chloride; 10 mM Magnesium chloride
Resolution 1.77 Å R-free 0.237
9ASG Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide analogue (Trp-6 Bta) Deposited 2024-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa） Fragment：extracellular domain
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；15% w/v Polyethylene glycol 3,350, 150mM Cesium chloride
Resolution 2.03 Å R-free 0.238
9CX0 Crystal structure of HLA-A*03:01 E152V mutant in complex with a mutant PIK3CA peptide Deposited 2024-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa）
Mutation：E152V GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277.15 K；12% w/v polyethylene glycol 3,350, 100 mM sodium malonate
Resolution 1.92 Å R-free 0.242
9CX1 Crystal structure of HLA-A*03:01 L156Q mutant in complex with a mutant PIK3CA peptide Deposited 2024-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa）
Mutation：L156Q GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；20% w/v polyethylene glycol 3,350, 200 mM sodium malonate
Resolution 2.00 Å R-free 0.221
9CX2 Crystal structure of HLA-A*03:01 L156Q mutant in complex with a mutant PIK3CA peptide Deposited 2024-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–298（274 aa）
Mutation：L156Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；10% w/v polyethylene glycol 20,000, 100 mM MES
Resolution 2.30 Å R-free 0.219
9NFC Structure of the cross-HLA supertype antibody R302 bound to a class I MHC presenting a divarasib-modified KRAS-G12C peptide on HLA-A*03 Deposited 2025-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 25–299（275 aa）
Not recorded A1AWR 1-{(3S)-4-[(7M)-7-[6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl]-6-chloro-8-fluoro-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}quinazolin-4-yl]-3-methylpiperazin-1-yl}propan-1-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot time 4 s blot force 5
Resolution 2.58 Å
9NW6 CA147v24 Fab bound to HLA-E-VL9 Deposited 2025-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 3–11（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M potassium iodide, 0.1 M MES pH 6.5, 25% PEG 4000
Resolution 3.10 Å R-free 0.258
9NW6 CA147v24 Fab bound to HLA-E-VL9 Deposited 2025-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 3–11（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M potassium iodide, 0.1 M MES pH 6.5, 25% PEG 4000
Resolution 3.10 Å R-free 0.258
9NW7 CA117v2v8 Fab bound to HLA-E-VL9 Deposited 2025-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 3–11（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG 3350
Resolution 2.10 Å R-free 0.233
9UV8 Crystal structure of HLA-A*11:01 in complex with KRAS G12D 9-mer peptide (VVGADGVGK) Deposited 2025-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；27% PEG3350,0.1M Bis-Tris,0.2M Lithium sulfate,additve 0.1M Spermidine
Resolution 1.79 Å R-free 0.231
9WVE Crystal structure of HLA-A*11:01 in complex with KRAS G12A 10-mer peptide (VVVGAAGVGK) Deposited 2025-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；23% PEG3350, 0.1M Bis-Tris, PH5.8, 0.2M Lithium sulfate
Resolution 2.80 Å R-free 0.267
9WVE Crystal structure of HLA-A*11:01 in complex with KRAS G12A 10-mer peptide (VVVGAAGVGK) Deposited 2025-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；23% PEG3350, 0.1M Bis-Tris, PH5.8, 0.2M Lithium sulfate
Resolution 2.80 Å R-free 0.267
9WVE Crystal structure of HLA-A*11:01 in complex with KRAS G12A 10-mer peptide (VVVGAAGVGK) Deposited 2025-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；23% PEG3350, 0.1M Bis-Tris, PH5.8, 0.2M Lithium sulfate
Resolution 2.80 Å R-free 0.267
9WVE Crystal structure of HLA-A*11:01 in complex with KRAS G12A 10-mer peptide (VVVGAAGVGK) Deposited 2025-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；23% PEG3350, 0.1M Bis-Tris, PH5.8, 0.2M Lithium sulfate
Resolution 2.80 Å R-free 0.267
9WVF Crystal structure of HLA-A*11:01 in complex with KRAS G12S 10-mer peptide (VVVGASGVGK) Deposited 2025-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate
Resolution 2.80 Å R-free 0.291
9WVF Crystal structure of HLA-A*11:01 in complex with KRAS G12S 10-mer peptide (VVVGASGVGK) Deposited 2025-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate
Resolution 2.80 Å R-free 0.291
9WVF Crystal structure of HLA-A*11:01 in complex with KRAS G12S 10-mer peptide (VVVGASGVGK) Deposited 2025-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate
Resolution 2.80 Å R-free 0.291
9WVF Crystal structure of HLA-A*11:01 in complex with KRAS G12S 10-mer peptide (VVVGASGVGK) Deposited 2025-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 25–299（275 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate
Resolution 2.80 Å R-free 0.291

53 other PDB entries and 78 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HLAA_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain P； PDBConstruct 2–33； UniProt 334–365 Author chain Y； PDBConstruct 2–33； UniProt 334–365

AP-1 complex subunit beta-1

Homo sapiens

UniProt Q10567

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain A； UniProt 1–949 Chain B； UniProt 1–949 Mutation：K359R, E476K ADP-ribosylation factor 1 × 4 （P84077） Protein Nef × 4 （Q90VU7） HLA class I histocompatibility antigen, A alpha chain × 2 （P04439） AP-1 complex subunit gamma-1 × 2 （P22892） AP-1 complex subunit mu-1 × 2 （P35585） AP-1 complex subunit sigma-3 × 2 （Q96PC3） GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments. cryo-EM vitrification conditions：Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted. Resolution 9.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8D4D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4HMY Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1 Deposited 2012-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–584（584 aa） Fragment：UNP residues 1-584
Mutation：I488F GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；288 K；0.2M lithium sulfate, 0.1M Tris pH 8.5, 0.2M lithium nitrate, 0.7M ammonium sulphate, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 7.00 Å R-free 0.250
4P6Z Crystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic domain bound to the clathrin adaptor protein complex 1 (AP1) core Deposited 2014-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–584（584 aa） Fragment：UNP residues 1-584
Mutation：T431A, E476K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7；298 K；Peg 6000, NaCl
Resolution 3.00 Å R-free 0.229
6CM9 Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit Deposited 2018-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 1–584（584 aa）
Mutation：K359R, E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
6CRI Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer Deposited 2018-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 24 PDB declaration: 24-meric
Chain B 14–583（570 aa）
Chain I 14–583（570 aa）
Chain J 14–583（570 aa）
Mutation：K359R, E476K Mutation：K359R, E476K Mutation：K359R, E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6D83 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer monomeric subunit Deposited 2018-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–584（584 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
6D84 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer Deposited 2018-04-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain B 1–584（584 aa）
Chain F 1–584（584 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
6DFF Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer Deposited 2018-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–584（584 aa）
Mutation：K359R, E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R4H phospho-STING binding to adaptor protein complex-1 Deposited 2022-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–584（584 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UX3 Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 2–949（948 aa）
Mutation：K359R,E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.60 Å
8D4C beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-06-01 Different construct Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 2–949（948 aa）
Chain B 2–949（948 aa）
Mutation：K359R, E476K Mutation：K359R, E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.30 Å
8D4E Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–949（949 aa）
Mutation：K359R, E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.20 Å
8D4F beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain A 1–949（949 aa）
Chain B 1–949（949 aa）
Mutation：K359R, E476K Mutation：K359R, E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.80 Å
8D4G gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain A 1–949（949 aa）
Chain B 1–949（949 aa）
Mutation：K359R, E476K Mutation：K359R, E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 11.60 Å
8D9R AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain A 1–949（949 aa）
Chain B 1–949（949 aa）
Chain D 1–949（949 aa）
Chain E 1–949（949 aa）
Chain F 1–949（949 aa）
Chain I 1–949（949 aa）
Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
8D9S AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain A 1–949（949 aa）
Chain B 1–949（949 aa）
Chain D 1–949（949 aa）
Chain E 1–949（949 aa）
Chain F 1–949（949 aa）
Chain I 1–949（949 aa）
Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9T AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain A 1–949（949 aa）
Chain B 1–949（949 aa）
Chain D 1–949（949 aa）
Chain E 1–949（949 aa）
Chain F 1–949（949 aa）
Chain I 1–949（949 aa）
Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9U AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain A 1–949（949 aa）
Chain B 1–949（949 aa）
Chain D 1–949（949 aa）
Chain E 1–949（949 aa）
Chain F 1–949（949 aa）
Chain I 1–949（949 aa）
Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9V gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes Deposited 2022-06-11 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 1–949（949 aa）
Chain B 1–949（949 aa）
Mutation：K359R,E476K Mutation：K359R,E476K GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.40 Å
8D9W beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain A 1–949（949 aa）
Chain B 1–949（949 aa）
Chain D 1–949（949 aa）
Chain E 1–949（949 aa）
Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K Mutation：K359R,E476K MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.30 Å

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AP1B1_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain A； PDBConstruct 1–949； UniProt 1–949 Author chain B； PDBConstruct 1–949； UniProt 1–949

AP-1 complex subunit gamma-1

Mus musculus

UniProt P22892

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain E； UniProt 1–595 Chain G； UniProt 1–595 Not recorded ADP-ribosylation factor 1 × 4 （P84077） Protein Nef × 4 （Q90VU7） HLA class I histocompatibility antigen, A alpha chain × 2 （P04439） AP-1 complex subunit beta-1 × 2 （Q10567） AP-1 complex subunit mu-1 × 2 （P35585） AP-1 complex subunit sigma-3 × 2 （Q96PC3） GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments. cryo-EM vitrification conditions：Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted. Resolution 9.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8D4D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GYU Gamma-adaptin appendage domain from clathrin adaptor AP1 Deposited 2002-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 703–821（119 aa） Fragment：APPENDAGE DOMAIN, RESIDUES 703-821
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；50MM HEPES PH7.4, 0.9M NA/K TARTRATE, 20% W/V GLYCEROL, pH 7.40
Resolution 1.81 Å R-free 0.223
1GYV Gamma-adaptin appendage domain from clathrin adaptor AP1, L762E mutant Deposited 2002-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 703–821（119 aa） Fragment：APPENDAGE DOMAIN, RESIDUES 703-821
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；50MM HEPES PH7.4,0.9M NA/K TARTRATE 20% W/V GLYCEROL, pH 7.40
Resolution 1.71 Å R-free 0.225
1GYW Gamma-adaptin appendage domain from clathrin adaptor AP1 A753D mutant Deposited 2002-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 694–821（128 aa） Fragment：APPENDAGE DOMAIN, RESIDUES 694-821
Mutation：YES CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；24% PEG4000, 100 MM TRIS PH 8.0, 200MM MGCL2, VAPOUR DIFFUSION
Resolution 2.40 Å R-free 0.269
1GYW Gamma-adaptin appendage domain from clathrin adaptor AP1 A753D mutant Deposited 2002-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 694–821（128 aa） Fragment：APPENDAGE DOMAIN, RESIDUES 694-821
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；24% PEG4000, 100 MM TRIS PH 8.0, 200MM MGCL2, VAPOUR DIFFUSION
Resolution 2.40 Å R-free 0.269
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 0–612（613 aa） Fragment：CORE, RESIDUES 0-612
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 0–612（613 aa） Fragment：CORE, RESIDUES 0-612
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 0–612（613 aa） Fragment：CORE, RESIDUES 0-612
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 0–612（613 aa） Fragment：CORE, RESIDUES 0-612
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain K 0–612（613 aa） Fragment：CORE, RESIDUES 0-612
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 0–612（613 aa） Fragment：CORE, RESIDUES 0-612
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
2A7B On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- The Optimal Data Collection Wavelength Deposited 2005-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 703–821（119 aa）
Not recorded XE XENON × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.65 Å R-free 0.228
3ZY7 Crystal structure of computationally redesigned gamma-adaptin appendage domain forming a symmetric homodimer Deposited 2011-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 704–822（119 aa） Fragment：COMPUTATIONALLY REDESIGNED GAMMA-ADAPTIN APPENDAGE DOMAIN, RESIDUES 704-822
Chain B 704–822（119 aa） Fragment：COMPUTATIONALLY REDESIGNED GAMMA-ADAPTIN APPENDAGE DOMAIN, RESIDUES 704-822
Mutation：YES Mutation：YES IPA ISOPROPYL ALCOHOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；PROTEIN SOLUTION: 20MM MES PH 6M 150MM NACL WELL SOLUTION: 0.1M NA ACETATE PH 5, 20% (W/V) PEG 8K, 6% (V/V) 2-PROPANOL CRYOPROTECTANT: WELL SOLUTION PLUS 15% (V/V) ETHYLENE GLYCOL
Resolution 1.09 Å R-free 0.181
4HMY Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1 Deposited 2012-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–595（595 aa） Fragment：UNP residues 1-595
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；288 K；0.2M lithium sulfate, 0.1M Tris pH 8.5, 0.2M lithium nitrate, 0.7M ammonium sulphate, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 7.00 Å R-free 0.250
4P6Z Crystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic domain bound to the clathrin adaptor protein complex 1 (AP1) core Deposited 2014-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 1–613（613 aa） Fragment：BST2/tetheirn cytoplasmic domain, UNP residues 1-613
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7；298 K；Peg 6000, NaCl
Resolution 3.00 Å R-free 0.229
6CM9 Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit Deposited 2018-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
6CRI Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer Deposited 2018-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 24 PDB declaration: 24-meric
Chain G 4–588（585 aa）
Chain Q 4–588（585 aa）
Chain R 4–588（585 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6D83 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer monomeric subunit Deposited 2018-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
6D84 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer Deposited 2018-04-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain G 1–595（595 aa）
Chain K 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
6DFF Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer Deposited 2018-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R4H phospho-STING binding to adaptor protein complex-1 Deposited 2022-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UX3 Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 2–595（594 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.60 Å
8D4C beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-06-01 Different construct Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain E 2–595（594 aa）
Chain G 2–595（594 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.30 Å
8D4E Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain G 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.20 Å
8D4F beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain E 1–595（595 aa）
Chain G 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.80 Å
8D4G gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain E 1–595（595 aa）
Chain G 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 11.60 Å
8D9R AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain G 1–595（595 aa）
Chain R 1–595（595 aa）
Chain T 1–595（595 aa）
Chain U 1–595（595 aa）
Chain V 1–595（595 aa）
Chain W 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
8D9S AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain G 1–595（595 aa）
Chain R 1–595（595 aa）
Chain T 1–595（595 aa）
Chain U 1–595（595 aa）
Chain V 1–595（595 aa）
Chain W 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9T AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain G 1–595（595 aa）
Chain R 1–595（595 aa）
Chain T 1–595（595 aa）
Chain U 1–595（595 aa）
Chain V 1–595（595 aa）
Chain W 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9U AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain G 1–595（595 aa）
Chain R 1–595（595 aa）
Chain T 1–595（595 aa）
Chain U 1–595（595 aa）
Chain V 1–595（595 aa）
Chain W 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9V gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes Deposited 2022-06-11 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain E 1–595（595 aa）
Chain G 1–595（595 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.40 Å
8D9W beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes Deposited 2022-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain K 1–595（595 aa）
Chain O 1–595（595 aa）
Not recorded MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.30 Å

25 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AP1G1_MOUSE
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 1–595； UniProt 1–595 Author chain G； PDBConstruct 1–595； UniProt 1–595

AP-1 complex subunit mu-1

Mus musculus

UniProt P35585

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain J； UniProt 1–423 Chain M； UniProt 1–423 Not recorded ADP-ribosylation factor 1 × 4 （P84077） Protein Nef × 4 （Q90VU7） HLA class I histocompatibility antigen, A alpha chain × 2 （P04439） AP-1 complex subunit beta-1 × 2 （Q10567） AP-1 complex subunit gamma-1 × 2 （P22892） AP-1 complex subunit sigma-3 × 2 （Q96PC3） GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments. cryo-EM vitrification conditions：Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted. Resolution 9.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8D4D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 1–423（423 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain N 1–423（423 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain O 1–423（423 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–423（423 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 1–423（423 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
1W63 AP1 clathrin adaptor core Deposited 2004-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 1–423（423 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE
Resolution 4.00 Å R-free 0.310
4EMZ HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain) Deposited 2012-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 158–423（266 aa） Fragment：sorting motif recognition domain
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Microbatch underoil；pH 6.5；298 K；0.1M HEPES, 3% PEG8000, pH 6.5, Microbatch underoil, temperature 298K
Resolution 2.90 Å R-free 0.278
4EMZ HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain) Deposited 2012-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 158–423（266 aa） Fragment：sorting motif recognition domain
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Microbatch underoil；pH 6.5；298 K；0.1M HEPES, 3% PEG8000, pH 6.5, Microbatch underoil, temperature 298K
Resolution 2.90 Å R-free 0.278
4EN2 HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain) Deposited 2012-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 158–423（266 aa） Fragment：sorting motif recognition domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch underoil；pH 6.5；298 K；0.1M HEPES, 3% PEG8000, pH 6.5, microbatch underoil, temperature 298K
Resolution 2.58 Å R-free 0.258
4EN2 HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain) Deposited 2012-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 158–423（266 aa） Fragment：sorting motif recognition domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch underoil；pH 6.5；298 K；0.1M HEPES, 3% PEG8000, pH 6.5, microbatch underoil, temperature 298K
Resolution 2.58 Å R-free 0.258
4HMY Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1 Deposited 2012-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain M 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；288 K；0.2M lithium sulfate, 0.1M Tris pH 8.5, 0.2M lithium nitrate, 0.7M ammonium sulphate, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 7.00 Å R-free 0.250
4P6Z Crystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic domain bound to the clathrin adaptor protein complex 1 (AP1) core Deposited 2014-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain M 1–423（423 aa） Fragment：Clathrin adaptor protein complex 1 (AP1) core, UNP residues 1-421
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7；298 K；Peg 6000, NaCl
Resolution 3.00 Å R-free 0.229
6CM9 Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit Deposited 2018-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain M 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
6CRI Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer Deposited 2018-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 24 PDB declaration: 24-meric
Chain M 2–423（422 aa）
Chain W 2–423（422 aa）
Chain X 2–423（422 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6D83 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer monomeric subunit Deposited 2018-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain M 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
6D84 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer Deposited 2018-04-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain M 1–423（423 aa）
Chain P 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
6DFF Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer Deposited 2018-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain M 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R4H phospho-STING binding to adaptor protein complex-1 Deposited 2022-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain M 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UX3 Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain M 2–423（422 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.60 Å
8D4C beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-06-01 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain J 1–423（423 aa）
Chain M 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.30 Å
8D4E Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain M 2–423（422 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.20 Å
8D4F beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain J 1–423（423 aa）
Chain M 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.80 Å
8D4G gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain J 1–423（423 aa）
Chain M 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 11.60 Å
8D9R AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain M 1–423（423 aa）
Chain j 1–423（423 aa）
Chain k 1–423（423 aa）
Chain l 1–423（423 aa）
Chain m 1–423（423 aa）
Chain n 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
8D9S AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain M 1–423（423 aa）
Chain j 1–423（423 aa）
Chain k 1–423（423 aa）
Chain l 1–423（423 aa）
Chain m 1–423（423 aa）
Chain n 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9T AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain M 1–423（423 aa）
Chain i 1–423（423 aa）
Chain j 1–423（423 aa）
Chain k 1–423（423 aa）
Chain l 1–423（423 aa）
Chain m 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9U AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain M 1–423（423 aa）
Chain i 1–423（423 aa）
Chain j 1–423（423 aa）
Chain k 1–423（423 aa）
Chain l 1–423（423 aa）
Chain m 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9V gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes Deposited 2022-06-11 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain J 1–423（423 aa）
Chain M 1–423（423 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.40 Å
8D9W beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain M 1–423（423 aa）
Chain X 1–423（423 aa）
Chain Z 1–423（423 aa）
Chain a 1–423（423 aa）
Not recorded MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.30 Å

22 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AP1M1_MOUSE
Isoform —
PDB entities 6
Chains and sequence ranges Author chain J； PDBConstruct 1–423； UniProt 1–423 Author chain M； PDBConstruct 1–423； UniProt 1–423

AP-1 complex subunit sigma-3

Homo sapiens

UniProt Q96PC3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain O； UniProt 1–154 Chain S； UniProt 1–154 Not recorded ADP-ribosylation factor 1 × 4 （P84077） Protein Nef × 4 （Q90VU7） HLA class I histocompatibility antigen, A alpha chain × 2 （P04439） AP-1 complex subunit beta-1 × 2 （Q10567） AP-1 complex subunit gamma-1 × 2 （P22892） AP-1 complex subunit mu-1 × 2 （P35585） GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments. cryo-EM vitrification conditions：Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted. Resolution 9.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8D4D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4HMY Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1 Deposited 2012-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；288 K；0.2M lithium sulfate, 0.1M Tris pH 8.5, 0.2M lithium nitrate, 0.7M ammonium sulphate, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 7.00 Å R-free 0.250
6CM9 Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit Deposited 2018-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
6CRI Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer Deposited 2018-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 24 PDB declaration: 24-meric
Chain S 1–142（142 aa）
Chain a 1–142（142 aa）
Chain b 1–142（142 aa）
Mutation：C148S Mutation：C148S Mutation：C148S GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6D83 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer monomeric subunit Deposited 2018-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
6D84 Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer Deposited 2018-04-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain Q 1–154（154 aa）
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
6DFF Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer Deposited 2018-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R4H phospho-STING binding to adaptor protein complex-1 Deposited 2022-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UX3 Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.60 Å
8D4C beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes Deposited 2022-06-01 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain O 1–154（154 aa）
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.30 Å
8D4E Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.20 Å
8D4F beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain O 1–154（154 aa）
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 9.80 Å
8D4G gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Deposited 2022-06-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain O 1–154（154 aa）
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
cryo-EM vitrification conditions Cryogen ETHANE；60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.
Resolution 11.60 Å
8D9R AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain S 1–154（154 aa）
Chain t 1–154（154 aa）
Chain u 1–154（154 aa）
Chain v 1–154（154 aa）
Chain w 1–154（154 aa）
Chain x 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
8D9S AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain S 1–154（154 aa）
Chain t 1–154（154 aa）
Chain u 1–154（154 aa）
Chain v 1–154（154 aa）
Chain w 1–154（154 aa）
Chain x 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 18 MG MAGNESIUM ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9T AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain S 1–154（154 aa）
Chain s 1–154（154 aa）
Chain t 1–154（154 aa）
Chain u 1–154（154 aa）
Chain v 1–154（154 aa）
Chain w 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9U AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on beta-Arf1 Deposited 2022-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain S 1–154（154 aa）
Chain s 1–154（154 aa）
Chain t 1–154（154 aa）
Chain u 1–154（154 aa）
Chain v 1–154（154 aa）
Chain w 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 20.00 Å
8D9V gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes Deposited 2022-06-11 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain O 1–154（154 aa）
Chain S 1–154（154 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.40 Å
8D9W beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes Deposited 2022-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain e 1–154（154 aa）
Chain f 1–154（154 aa）
Not recorded MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.30 Å
9DDT AAGAB pseudoGTPase domain in complex with AP-1 clathrin adaptor complex sigma 3 subunit Deposited 2024-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–154（154 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1M Bis-Tris pH 6.5, 25% PEG3350
Resolution 1.68 Å R-free 0.211

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AP1S3_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain O； PDBConstruct 1–154； UniProt 1–154 Author chain S； PDBConstruct 1–154； UniProt 1–154

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8d4d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8d4d
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▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8d4d
Deposition date deposition_date2022-06-01
Structure title titlegamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes
Keywords keywordsnef, AP, trafficking, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier75.81 Å
Radius of gyration Rg (electron density) rg_electron76.41 Å
Forward intensity I(0) i02392530000.00
Molecular weight molecular_weight253000.0 kDa
Excluded volume excluded_volume248130 ų
Envelope volume envelope_volume842980 ų
Hydration-shell volume shell_volume97583 ų
Envelope diameter envelope_diameter249.1 Å
Shell Rg shell_rg65.74 Å
Envelope Rg envelope_rg73.16 Å
Shape Rg shape_rg76.42 Å
Total Rg total_rg76.22 Å
Total atoms total_atoms18028
Residues n_residues4474
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax219.8 Å
Rg (real space) rg_real76.11 Å
Rg uncertainty (real space) rg_real_error1.42 Å
I(0) (real space) i0_real2.3910e+09
I(0) uncertainty (real space) i0_real_error4.6740e+07
Rg (reciprocal space) rg_reciprocal73.95 Å
I(0) (reciprocal space) i0_reciprocal2381000000.0000
Solution quality estimate total_estimate0.8275
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary62.8 Å
Skewness Skewness skewness0.402
Kurtosis Kurtosis kurtosis-0.758
Angular range angular_range— – 0.1050 Å−1
Current regularization parameter α current_alpha0.0034
Highest regularization parameter α highest_alpha130700000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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8. Citations (1)

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9. Files and Curves (10)